Contacts of the helix formed by residues 184 - 193 (chain D) in PDB entry 3ORH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 184 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178D MET* 3.6 3.1 - - - +
182D TYR* 3.6 2.2 - - - +
183D SER* 1.3 81.7 + - - +
185D ILE* 1.4 58.7 + - - +
186D THR* 3.0 22.0 + - - -
187D ILE* 3.1 33.0 + - + +
188D MET* 3.1 26.3 + - - +
225D PHE* 4.8 0.4 - - - -
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Residues in contact with ILE 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D TRP* 5.7 1.1 - - + -
178D MET* 3.6 17.6 - - + +
183D SER 4.3 0.2 + - - -
184D ASP* 1.4 70.0 + - - +
186D THR* 1.4 62.4 + - - +
188D MET* 3.5 14.0 + - + +
189D PHE* 3.1 27.4 + - - +
211D VAL* 3.8 26.5 - - + -
223D TYR* 3.4 25.4 - - - +
225D PHE* 3.9 14.7 - - + -
227D GLN* 3.4 34.9 + - - +
228D MET 3.9 0.4 - - - -
229D ILE* 3.8 34.4 - - + +
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Residues in contact with THR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ASP* 3.0 8.9 + - - -
185D ILE* 1.4 74.9 - - - +
187D ILE* 1.4 62.0 + - + +
189D PHE* 3.4 3.6 + - + +
190D GLU* 2.9 32.8 + - + +
209D THR* 4.5 17.7 - - + +
211D VAL* 3.6 22.9 - - - +
229D ILE* 3.9 8.5 - - + +
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Residues in contact with ILE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D TYR* 3.9 15.9 - - + -
184D ASP* 3.1 37.0 + - + +
186D THR* 1.4 74.9 - - + +
188D MET* 1.3 64.4 + - - +
190D GLU* 3.2 7.8 + - + +
191D GLU* 2.9 46.4 + - + +
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Residues in contact with MET 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D TRP* 3.6 50.5 - - + +
177D LEU* 4.0 14.1 - - + -
178D MET* 3.7 20.4 - - - -
182D TYR* 3.6 38.8 - - + -
184D ASP 3.1 6.2 + - - +
185D ILE* 3.5 27.6 - - + +
187D ILE* 1.3 75.8 - - - +
189D PHE* 1.3 63.7 + - - +
191D GLU 3.9 0.2 - - - -
192D THR* 2.8 51.5 + - - +
193D GLN* 4.5 0.2 - - - -
229D ILE* 4.5 5.4 - - + -
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Residues in contact with PHE 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D TYR* 3.6 24.7 - + - -
174D TRP* 4.3 7.4 - + - -
185D ILE 3.1 14.2 + - - +
186D THR* 3.6 8.5 - - + +
188D MET* 1.3 80.0 - - + +
190D GLU* 1.3 60.8 + - - +
193D GLN* 2.9 44.4 + - + +
194D VAL* 3.2 28.3 + - + -
197D LEU* 3.8 15.7 - - + -
204D ARG* 6.2 0.2 - - - -
207D ILE* 4.2 11.9 - - + -
208D ARG 5.4 0.2 - - - -
209D THR* 5.0 11.0 - - + -
229D ILE* 3.9 30.1 - - + -
231D PRO* 3.6 36.8 - - + -
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Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D THR* 2.9 22.8 + - + +
187D ILE* 3.2 9.8 + - + +
189D PHE* 1.3 80.8 - - - +
191D GLU* 1.3 63.2 + - + +
194D VAL* 3.4 35.5 - - - +
195D PRO* 3.6 6.8 - - - +
204D ARG* 2.9 42.6 + - - -
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Residues in contact with GLU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D TYR* 2.8 42.9 + - + +
187D ILE* 2.9 30.7 + - + +
190D GLU* 1.3 81.3 - - + +
192D THR* 1.3 59.7 + - - +
193D GLN 3.7 0.2 - - - -
195D PRO* 3.8 15.1 - - - +
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Residues in contact with THR 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D PHE* 3.3 21.3 - - - -
177D LEU* 4.2 15.2 - - + +
182D TYR* 3.5 32.5 - - + +
188D MET* 2.8 29.2 + - - +
191D GLU* 1.3 77.0 - - + +
193D GLN* 1.3 78.8 + - - +
195D PRO* 4.4 3.1 - - - +
196D ALA* 5.2 1.6 - - - +
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Residues in contact with GLN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D HIS 5.0 2.2 + - - -
148D GLN* 3.0 23.5 + - - +
149D PHE* 3.3 15.1 - - - -
168D TYR* 2.9 29.6 + - - +
173D SER* 5.2 1.0 + - - -
174D TRP* 3.2 26.4 - - + +
177D LEU* 5.0 2.4 - - - +
188D MET* 4.7 0.4 - - - -
189D PHE* 2.9 44.9 + - + +
192D THR* 1.3 107.1 + - - +
194D VAL* 1.3 64.7 + - - +
195D PRO* 3.4 2.2 - - - -
196D ALA* 3.3 8.4 + - - +
197D LEU* 3.2 21.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il